Genetics Commons^™

Testing Gene-Environment Interactions In The Presence Of Measurement Error, Chongzhi Di, Li Hsu, Charles Kooperberg, Alex Reiner, Ross Prentice

UW Biostatistics Working Paper Series

Complex diseases result from an interplay between genetic and environmental risk factors, and it is of great interest to study the gene-environment interaction (GxE) to understand the etiology of complex diseases. Recent developments in genetics field allows one to study GxE systematically. However, one difficulty with GxE arises from the fact that environmental exposures are often measured with error. In this paper, we focus on testing GxE when the environmental exposure E is subject to measurement error. Surprisingly, contrast to the well-established results that the naive test ignoring measurement error is valid in testing the main effects, we find that …

Cloning And Characterization Of Il-1Β, Il-8, Il-10, And Tnfα From Golden Tilefish (Lopholatilus Chamaeleonticeps) And Red Snapper (Lutjanus Campechanus), Kristina L. Deak

USF Tampa Graduate Theses and Dissertations

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines …

Fisheries Management Paper No.266 - Exmouth Gulf Prawn Managed Fishery Bycatch Action Plan 2014-2019. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Bycatch is described as the part of the catch which is returned to the sea (usually referred to as non-retained or discarded) either because it has no commercial value or because legislative requirements preclude it being retained. Thus, this Bycatch Action Plan (BAP) includes unmarketable finfish and invertebrate species, along with endangered, threatened and protected (ETP) species, such as marine mammals, reptiles and some elasmobranchs.

It is Government policy to minimise bycatch in all commercial fisheries. This BAP details a program of actions to address bycatch issues in the Exmouth Gulf Prawn Managed Fishery (EGPMF), in accordance with the EGPMF …

Intercellular Cooperation And Competition In Brain Cancers: Lessons From Drosophila And Human Studies, Indrayani Waghmare, Austin Roebke, Mutsuko Minata, Madhuri Kango-Singh, Ichiro Nakano

Biology Faculty Publications

Glioblastoma (GBM) is a primary brain cancer with an extremely poor prognosis. GBM tumors contain heterogeneous cellular components, including a small subpopulation of tumor cells termed glioma stem cells (GSCs). GSCs are characterized as chemotherapy- and radiotherapy-resistant cells with prominent tumorigenic ability. Studies in Drosophila cancer models demonstrated that interclonal cooperation and signaling from apoptotic clones provokes aggressive growth of neighboring tumorigenic clones, via compensatory proliferation or apoptosis induced proliferation. Mechanistically, these aggressive tumors depend on activation of Jun-N-terminal kinase (upstream of c-JUN), and Drosophila Wnt (Wg) in the apoptotic clones. Consistent with these nonmammalian studies, data from several mammalian …

Legume Crops Phylogeny And Genetic Diversity For Science And Breeding, Petr Smýkal, Clarice J. Coyne, Mike J. Ambrose, Nigel Maxted, Hanno Schaefer, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, …

Scalable Combinatorial Tools For Health Disparities Research, Michael A. Langston, Robert S. Levine, Barbara J. Kilbourne, Gary L. Rogers Jr., Anne D. Kershenbaum, Suzanne H. Baktash, Steven S. Coughlin, Arnold M. Saxton, Vincent K. Agboto, Darryl B. Hood, Maureen Y. Litchveld, Tonny J. Oyana, Patricia Matthews-Juarez, Paul D. Juarez

Sociology Faculty Research

Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size …

Genetic Analysis Of Ton2 Dependent Processes In Microtubule Organization In Arabidopsis Thaliana, Samantha Nicole Atkinson

Theses and Dissertations

Microtubules carry out many functions within the cell. They're used during mitosis and meiosis to move chromosomes to opposite sides of the cell so that cell division can occur. They're also used as structural support for the cell and are involved in establishing the cell shape. Microtubules are also able to reorient from a longitudinal orientation to a transverse orientation in response to gibberellic acid and auxin (two hormones that are involved in cell elongation). The mechanism for how this reorientation occurs is unknown. The TONNEAU2 (TON2) protein is necessary for proper microtubule organization. We looked at how TON2 affects …

Analysis Of Differential Mrna And Mirna Expression In An Alzheimer’S Disease Mouse Model, Amanda Hazy, Matthew Dalton

Other Undergraduate Scholarship

Research has shown that changes in gene expression play a critical role in the development of Alzheimer’s Disease (AD). Our project will evaluate genome-wide RNA expression patterns from brain and blood in an AD mouse model. This analysis will provide insight regarding the mechanisms of AD pathology as well as determine a possible diagnostic tool utilizing RNA expression patterns found in the blood as biomarkers for AD.

The Peopling Of The African Continent And The Diaspora Into The New World, Michael Campbell, Jibril Hirbo, Jeffrey Peter Townsend, Sarah Tishkoff

Department of Biology Faculty Publications

Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will …

Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang

Open Access Dissertations

DNA methylation is a key epigenetic mark for transcriptional gene silencing in many eukaryotes. DNA methylation status can be dynamically controlled by methylation and active demethylation processes. Compared to the well-known mechanisms of DNA methylation, the mechanisms of DNA demethylation and its regulation are poorly understood. In order to better understand the DNA demethylation pathway, we developed two genetic screening systems in Arabidopsis to identify new components involved in the DNA demethylation. In the first system, which is based on 35S promoter driven SUC2 (sucrose transporter 2) transgene, a mutant (91-1) was isolated and map-based cloning identified the …

Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad

Open Access Dissertations

Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …

Tbx5 Is Required For Avian And Mammalian Epicardial Formation And Coronary Vasculogenesis., Nata Y Diman, Gabriel Brooks, Boudewijn P Kruithof, Olivier Elemento, Jonathan G Seidman, Christine Seidman, Craig T Basson, Cathy J. Hatcher

PCOM Scholarly Works

Rationale: Holt-Oram syndrome (HOS) is an autosomal dominant heart-hand syndrome caused by mutations in the TBX5 gene. Overexpression of Tbx5 in the chick proepicardial organ (PEO) impaired coronary blood vessel formation. However, the potential activity of Tbx5 in the epicardium itself, and Tbx5's role in mammalian coronary vasculogenesis, remains largely unknown. Objective: To evaluate the consequences of altered Tbx5 gene dosage during PEO and epicardial development in the embryonic chick and mouse. Methods and Results: Retroviral-mediated knockdown or upregulation of Tbx5 expression in the embryonic chick PEO as well as proepicardial-specific deletion of Tbx5 in the embryonic mouse (Tbx5(epi-/-)) impaired …

Genetic Genealogy: What Every Librarian Should Know, Rosemary L. Meszaros, Katherine Pennavaria

DLPS Faculty Publications

The past few years television, podcasts, and blogs across the Internet promoted the role of DNA testing in genealogy. But what do you really get, and is it worth the price? We discuss the logistics of DNA testing as it relates to genealogy and take a hard look at the legal issues involved in genealogy’s hottest topic.

Haplotype Variety Analysis Of Human Populations: An Application To Hapmap Data, Michelle Creek, Cyril Rakovski

e-Research: A Journal of Undergraduate Work

We undertake a study to investigate the haplotype variety of distinct human populations. We use a natural measure of haplotype variety, the total number of haplotypes (TNH) present that reflects the number of haplotypes with nonzero frequencies estimated from the data at hand for each selection of multiple loci. For the analysis of real human populations, we use the haplotype data of the Denver Chinese, Tuscan Italians, Luhya Kenyans, and Gujarati Indians from release III of the HapMap database. Moreover, we show that the TNH statistic is biased in small sample data scenarios such as the HapMap and implement a …

On The Ranking Of The Disease Susceptibility Locus In Family-Based Candidate Gene Studies: A Simulation-Based Analysis, Lisa A. Brown, Cyril Rakovski

e-Research: A Journal of Undergraduate Work

The ranking of the p-value of the true causal single nucleotide polymorphism in the ordered list of individual SNP p-values is an important factor for achieving success in the ultimate objective of association studies - identifying deleterious genetic variants. Thus, we undertake a study to assess the implications of complex, multimarker correlation structure, sample size and disease models on the ranking of the causal SNP. We carry out an extensive family-based candidate gene simulation study to analyze the position of the disease susceptibility locus in the complete list of individual SNP p-values ordered according to their statistical significance. We simulate …

Nsf Bets Big On David Angelini, Gerry Boyle

Colby Magazine

Something has been bugging Colby geneticist David Angelini.

How, Angelini wonders, can a single species (in this case the soapberry bug) produce two distinctly different forms, one with long wings and one with short, that are not linked to sex? What is the genetic mechanism that causes the wings to develop differently?

"Why does it not overshoot the long form? he asked. "Why doesn't it undershoot the short form? Why doesn't it end up somewhere in the middle? That's an open question."

And a question that the National Science Foundation wants him to answer.

A Homogenizing Process Of Selection Has Maintained An 'Ultra-Slow' Acetylation Nat2 Variant In Humans, Blandine Patillon, Pierre Luisi, Estella S. Poloni, Sotiria Boukouvala, Pierre Darlu, E. Genin, Audrey Sabbagh

Human Biology Open Access Pre-Prints

N-acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of the whole-genome sequence data available from the 1000 Genomes project to investigate the …

Hla Class Ii Alleles In The Otomi Population Of The Mezquital Valley. A Genetic Approach To The History Of Interethnic Migrations In The Mexican Central Plateau, Ana Itzel Juárez-Martín, Blanca Zoila González-Sobrino, Ángel Eduardo Camarena Olvera, Ramcés Falfán-Valencia

Human Biology Open Access Pre-Prints

From a historic and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the making of the population dynamics of the Mexican Central Plateau. Due to their antiquity in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua.

This study analyzes the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intra-regional level historical perspective of the genetic relationships between the Otomi of the …

Estimating Migration Rates Between Populations Of Zostera Marina In The San Francisco Bay, Elizabeth S. Gutierrez

STAR Program Research Presentations

Eelgrass (Zostera marina) is a highly clonal marine angiosperm that can also reproduce sexually through flowering and seed formation. In a previous study, Fst values from six microsatellite loci suggested that a perennial San Francisco Bay subpopulation at Point Molate (Richmond, California) was able to recover from a drastic 2006 die-off through seed recruitment from neighboring eelgrass subpopulations, changing its reproductive strategy from clonal to sexual. Although Fst measures continue to be widely used in population genetics, the assumptions under which they operate are not always appropriate given certain circumstances, such small population sizes and/or asymmetrical migration rates. Our summer …

The Trehalose Pathway In Maize: Conservation And Gene Regulation In Response To The Diurnal Cycle And Extended Darkness, Clémence Henry, Samuel W. Bledsoe, Allison Siekman, Alec Kollman, Brian M. Waters, Regina Feil, Mark Stitt, L. Mark Lagrimini

Department of Agronomy and Horticulture: Faculty Publications

Energy resources in plants are managed in continuously changing environments, such as changes occurring during the day/night cycle. Shading is an environmental disruption that decreases photosynthesis, compromises energy status, and impacts on crop productivity. The trehalose pathway plays a central but not well-defined role in maintaining energy balance. Here, we characterized the maize trehalose pathway genes and deciphered the impacts of the diurnal cycle and disruption of the day/night cycle on trehalose pathway gene expression and sugar metabolism. The maize genome encodes 14 trehalose-6-phosphate synthase (TPS) genes, 11 trehalose-6-phosphate phosphatase (TPP) genes, and one trehalase gene. Transcript abundance of most …